Clustal Omega is a multiple sequence alignment program. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms.Input parameters for the toolOutput guide tree [Output guide tree.]Output distance matrix [Output distance matrix. This is only calculated if the mBed-like clustering guide tree is set to false.]Dealign input sequences [Remove any existing alignment (gaps) from input sequences.]mBed-like clustering guide tree [This option uses a sample of the input sequences and then represents all sequences as vectors to these sequences, enabling much more rapid generation of the guide tree, especially when the number of sequences is large.]mBed-like clustering iteration [Use mBed-like clustering during subsequent iterations.]Number of iterations [Number of (combined guide-tree/HMM) iterations.]Maximum guide tree iterations [Having set the number of combined iterations, this parameter can be changed to limit the number of guide tree iterations within the combined iterations.]Maximum HMM iterations [Having set the number of combined iterations, this parameter can be changed to limit the number of HMM iterations within the combined iterations.]Output alignment format [Format for generated multiple sequence alignment.]Output order [The order in which the sequences appear in the final alignment]Sequence Type [Defines the type of the sequences to be aligned]Sequence [Three or more sequences to be aligned can be entered directly into this box. Sequences can be in GCG, FASTA, EMBL (Nucleotide only), GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot (Protein only) format. Partially formatted sequences are not accepted. Adding a return to the end of the sequence may help certain applications understand the input. Note that directly using data from word processors may yield unpredictable results as hidden/control characters may be present.
There is currently a sequence input limit of 4000 sequences and 4MB of data.
]List of renderers available to output the result of the jobDetails about a renderer used to output the result of the jobA short description of the rendererA suggested file suffix to be used when saving the data formatted by the rendererThe renderer identifier to be used when invoking the getResult() methodA more appropriate name for the renderer (more meaningful than the identifier)The media type (MIME) of the renderer's outputA set of parameters passed to a renderer when formatting the dataA parameter used by the rendererThe name of the parameterThe parameter value as an array of StringList the names of the tool parametersDetails about a tool parameterThe name of the parameterA short description of the parameterThe type of the parameterThe list of values available for this parameterThe list of parameter valuesThe details about a parameter valuesA meaningful label for the parameter valueThe real valueA flag indicating whether this value is a default value or notA set of additional properties associated with the parameter valueA set of propertiesA key/value pair association of informationUser email addressA title to identify the analysis jobThe list of parameters to be used for launching the analysisA unique identifier for the analysis jobAn identifier for the job to checkThe status of the job (FINISHED, ERROR, RUNNING, NOT_FOUND or FAILURE)An identifier for the job to checkThe list of renderers availableAn identifier for the job to checkThe renderer to be used to format the outputA list of parameters to be passed on to the rendererBase64 encoded data corresponding to the output of the job formatted by the rendererThe identifier for the parameterThe parameter detailsThe list of parameters available for this toolSubmit an analysis jobGet the status of a submitted jobGet the list of renderers available to output a job result (i.e. the list of available output types)Get a job result formatted using a particular rendererList the names of the parameters available before submissionGet some details about a parameter (e.g. name, description, values, etc.)Submit an analysis job

Get the status of a submitted job

Get the list of renderers available to output a job result (i.e. the list of available output types)

Get a job result formatted using a particular renderer

List the names of the parameters available before submission

Get some details about a parameter (e.g. name, description, values, etc.)